Improved Algorithms for Macromolecular Structure Determination by cyro-EM

冷冻电镜大分子结构测定的改进算法

• 批准号: 8761618
• 负责人: Amit Singer
• 金额: $ 33.78万
• 依托单位: PRINCETON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2018-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8761618
• 关键词: Algorithms; Area; Biological; Biological Process; Classification; Complex; Computational algorithm; Computer software; Cryoelectron Microscopy; Crystallization; Data; Data Set; Detection; Development; Drug Design; Electron Microscope; Electron Microscopy; Electrons; Exhibits; Failure; Freezing; Goals; Heterogeneity; Ice; Image; Individual; Investigation; Lead; Linear Algebra; Liquid substance; Macromolecular Complexes; Methods; Molecular; Molecular Conformation; Molecular Structure; Motion; Names; Nitrogen; Noise; Output; Particle Size; Performance; Population; Positioning Attribute; Preparation; Proteins; Research; Resolution; Resort; Rotation; Sampling; Signal Transduction; Simulate; Specimen; Staining method; Stains; Structure; Techniques; Temperature; Universities; Validation; Variant; X-Ray Crystallography; base; computer framework; cost; heuristics; image processing; improved; insight; interest; macromolecule; novel; novel strategies; open source; particle; polypeptide; programs; protein structure; public health relevance; reconstruction; signal processing; structural biology; success; theories; three dimensional structure

DESCRIPTION (provided by applicant): Single-particle electron cryomicroscopy (cryo-EM) is a method for observing the three- dimensional structures of large macromolecules. In cryo-EM the experimental data consist of noisy, random projection images of macromolecular "particles", and the problem is finding the 3D structure which is consistent with these images. The proposal aims to develop and apply to experimental data novel algorithms for solving two difficult mathematical problems posed by this technique of structural biology. First, classical cryo-EM reconstruction techniques assume that the particles are identical. However, in many datasets this assumption does not hold. Some molecules of interest have more than one conformational state. These structural variations are of great interest to biologists, as they provide insight int the functioning of the molecule. The first area of investigation in this project is the development of algorithmic and mathematical framework for determining structures associated with heterogeneous particle populations. The proposed algorithm is not only faster than existing techniques but is also mathematically provable to reveal the different conformations if the number of images is sufficiently large. Second, a major limiting factor for present cryo-EM studies is the particle size. Images of small particles are often too noisy for existing methods to provide valid three-dimensional reconstructions; although the images contain structural information, the assignment of orientations to the individual particles is unreliable. The second area of investigation focuses on developing a radical new approach for reconstruction of small particles without the need for determining particle orientations.

描述（由申请人提供）：单粒子电子低温显微镜（cryo-EM）是一种用于观察大分子三维结构的方法。在冷冻EM实验数据包括嘈杂的，随机投影图像的大分子“颗粒”，问题是找到的3D结构，这是符合这些图像。该提案的目的是开发和应用实验数据的新算法，以解决这种结构生物学技术所带来的两个困难的数学问题。首先，经典的cryo-EM重建技术假设粒子是相同的。然而，在许多数据集中，这个假设并不成立。一些感兴趣的分子具有多于一种构象状态。这些结构变异引起了生物学家的极大兴趣，因为它们提供了对分子功能的深入了解。该项目的第一个调查领域是开发 的算法和数学框架，用于确定结构与异质粒子群体。该算法不仅比现有技术更快，而且在数学上可以证明，如果图像的数量足够大，则可以揭示不同的构象。其次，目前冷冻EM研究的主要限制因素是颗粒尺寸。小颗粒的图像通常太嘈杂，现有方法无法 提供有效的三维重建;虽然图像包含结构信息，但单个颗粒的取向分配是不可靠的。第二个领域的调查重点是开发一个激进的新方法重建的小颗粒，而不需要确定颗粒的取向。